Contacts of the helix formed by residues 308 - 318 (chain E) in PDB entry 2ONK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 308 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304E LYS 2.8 19.4 + - - -
305E LEU* 3.1 18.9 + - - +
307E ILE* 1.3 78.2 - - - +
309E GLU* 1.3 63.8 + - - +
310E GLU* 3.2 21.2 + - - +
311E GLY 3.0 2.8 + - - -
312E GLN* 2.9 16.3 + - - +
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Residues in contact with GLU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E SER* 1.3 72.2 - - - +
310E GLU* 1.3 65.6 + - - +
312E GLN* 2.9 22.3 + - - +
313E GLU* 2.7 31.3 + - + +
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Residues in contact with GLU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ALA* 4.4 14.7 - - + +
305E LEU* 3.0 24.8 - - + +
308E SER* 3.1 10.7 + - - +
309E GLU* 1.3 78.1 - - - +
311E GLY* 1.3 58.6 + - - +
313E GLU* 3.1 6.0 + - - +
314E ILE* 2.8 41.1 + - + +
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Residues in contact with GLY 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E PHE* 3.8 13.9 - - - -
305E LEU* 3.3 22.3 + - - +
306E VAL 3.5 9.9 - - - -
308E SER 3.0 5.3 + - - -
310E GLU* 1.3 79.6 - - - +
312E GLN* 1.3 62.3 + - - +
314E ILE* 3.1 9.2 + - - +
315E LEU* 3.0 27.6 + - - +
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Residues in contact with GLN 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E VAL 4.0 2.8 + - - +
307E ILE* 3.2 20.5 + - - +
308E SER 2.9 13.9 + - - +
309E GLU* 2.9 24.1 + - - +
311E GLY* 1.3 73.4 - - - +
313E GLU* 1.3 57.1 + - + +
315E LEU* 3.8 1.5 + - - -
316E ARG* 3.1 29.3 + - - +
322E PRO* 3.3 35.4 - - + +
323E LEU 4.6 2.0 + - - -
324E VAL* 3.4 40.2 - - + +
326E PRO* 4.3 13.1 - - - +
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Residues in contact with GLU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E GLU* 2.7 23.0 + - + +
310E GLU* 3.6 6.1 - - - +
312E GLN* 1.3 70.5 - - + +
314E ILE* 1.3 57.0 + - - +
316E ARG* 2.6 39.9 + - - +
317E GLU* 2.6 63.0 + - + +
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Residues in contact with ILE 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PRO* 4.1 8.3 - - + +
49E ALA* 3.5 40.4 - - + +
50E PHE* 3.9 38.1 - - + +
53E ALA* 4.3 13.5 - - + -
305E LEU* 5.1 1.1 - - + -
310E GLU* 2.8 25.2 + - + +
311E GLY* 3.1 11.9 - - - +
313E GLU* 1.3 78.0 - - - +
315E LEU* 1.3 68.4 + - - +
317E GLU* 3.0 19.9 + - - +
318E LEU* 3.1 10.8 + - + +
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Residues in contact with LEU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 4.5 5.4 - - + -
46E PRO* 4.0 18.2 - - + -
50E PHE* 3.7 22.2 - - + -
110E PHE* 3.9 32.3 - - + +
111E ALA* 4.1 2.7 - - + -
306E VAL 4.8 3.4 - - - +
311E GLY 3.0 15.1 + - - +
312E GLN* 3.8 4.5 - - - +
314E ILE* 1.3 82.5 - - - +
316E ARG* 1.3 60.8 + - - +
318E LEU* 3.0 14.5 + - - +
320E GLN* 2.9 67.1 + - + +
322E PRO* 4.0 11.4 - - + -
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Residues in contact with ARG 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E GLN* 3.1 27.3 + - - +
313E GLU* 2.6 43.1 + - - +
315E LEU* 1.3 75.8 - - - +
317E GLU* 1.3 65.9 + - - +
319E GLY* 3.1 12.3 + - - -
320E GLN 3.2 10.9 + - - +
321E GLU* 4.2 21.5 + - - +
322E PRO* 3.1 31.1 + - + +
324E VAL* 4.1 4.4 - - - +
263J GLU* 3.4 31.6 + - - -
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Residues in contact with GLU 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLU* 2.6 44.7 + - + +
314E ILE* 3.1 13.2 - - - +
316E ARG* 1.3 73.9 - - - +
318E LEU* 1.3 65.6 + - + +
319E GLY 3.1 4.2 + - - -
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLU* 3.5 15.3 - - + +
46E PRO* 3.2 47.1 - - + +
49E ALA* 4.8 5.4 - - + -
238E SER 3.7 3.1 - - - +
241E LYS* 5.2 1.2 - - - +
242E GLN* 3.3 37.2 + - + +
314E ILE* 3.6 15.0 - - + +
315E LEU 3.0 8.5 + - - +
317E GLU* 1.3 81.2 - - + +
319E GLY* 1.3 62.1 + - - +
320E GLN* 3.2 2.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il